Merge pull request #49 from PF2-pasteur-fr/development

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PF2-pasteur-fr · Jun 1, 2018 · e9aae7a · e9aae7a
2 parents b5fa8e8 + 8d1425c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: SARTools
 Type: Package
 Title: Statistical Analysis of RNA-Seq Tools
-Version: 1.6.2
-Date: 2018-05-23
+Version: 1.6.3
+Date: 2018-06-01
 Author: Marie-Agnes Dillies and Hugo Varet
 Maintainer: Hugo Varet <[email protected]>
 Depends: R (>= 3.3.0), DESeq2 (>= 1.12.0), edgeR (>= 3.12.0), xtable

diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+CHANGES IN VERSION 1.6.3
+------------------------
+	o now allows fitType="mean" in DESeq2
+
 CHANGES IN VERSION 1.6.2
 ------------------------
 	o fixed a bug in template_script_edgeR_CL.r to use forceCairoGraph option

diff --git a/R/checkParameters.DESeq2.r b/R/checkParameters.DESeq2.r
@@ -60,8 +60,8 @@ checkParameters.DESeq2 <- function(projectName,author,targetFile,rawDir,
     message("batch must be NULL or a character vector of length 1")
     problem <- TRUE
   }
-  if (!is.character(fitType) | length(fitType)!=1 || !I(fitType %in% c("parametric","local"))){
-    message("fitType must be equal to 'parametric' or 'local'")
+  if (!is.character(fitType) | length(fitType)!=1 || !I(fitType %in% c("parametric","local","mean"))){
+    message("fitType must be equal to 'parametric', 'local', or 'mean'")
     problem <- TRUE
   }
   if (!is.logical(cooksCutoff) | length(cooksCutoff)!=1){

diff --git a/inst/report_DESeq2.rmd b/inst/report_DESeq2.rmd
@@ -167,7 +167,7 @@ Model outliers are features for which at least one sample seems unrelated to the
 
 ## Dispersions estimation
 
-The DESeq2 model assumes that the count data follow a negative binomial distribution which is a robust alternative to the Poisson law when data are over-dispersed (the variance is higher than the mean). The first step of the statistical procedure is to estimate the dispersion of the data. Its purpose is to determine the shape of the mean-variance relationship. The default is to apply a GLM (Generalized Linear Model) based method (fitType="parametric"), which can handle complex designs but may not converge in some cases. The alternative is to use fitType="local" as described in the original paper [@Anders2010]. The parameter used for this project is fitType="`r fitType`". Then, DESeq2 imposes a Cox Reid-adjusted profile likelihood maximization [@cox1897 and McCarthy, 2012] and uses the maximum _a posteriori_ (MAP) of the dispersion [Wu, 2013].
+The DESeq2 model assumes that the count data follow a negative binomial distribution which is a robust alternative to the Poisson law when data are over-dispersed (the variance is higher than the mean). The first step of the statistical procedure is to estimate the dispersion of the data. Its purpose is to determine the shape of the mean-variance relationship. The default is to apply a GLM (Generalized Linear Model) based method (fitType="parametric"), which can handle complex designs but may not converge in some cases. The alternative is to use fitType="local" as described in the original paper [@Anders2010] or fitType="mean". The parameter used for this project is fitType="`r fitType`". Then, DESeq2 imposes a Cox Reid-adjusted profile likelihood maximization [@cox1897 and McCarthy, 2012] and uses the maximum _a posteriori_ (MAP) of the dispersion [Wu, 2013].
 
 
 <center>

diff --git a/template_script_DESeq2.r b/template_script_DESeq2.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.2
+### designed to be executed with SARTools 1.6.3
 ################################################################################
 
 ################################################################################

diff --git a/template_script_DESeq2_CL.r b/template_script_DESeq2_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and DESeq2 packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.2
+### designed to be executed with SARTools 1.6.3
 ### run "Rscript template_script_DESeq2_CL.r --help" to get some help
 ################################################################################
 

diff --git a/template_script_edgeR.r b/template_script_edgeR.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### March 20th, 2018
-### designed to be executed with SARTools 1.6.2
+### designed to be executed with SARTools 1.6.3
 ################################################################################
 
 ################################################################################

diff --git a/template_script_edgeR_CL.r b/template_script_edgeR_CL.r
@@ -2,7 +2,7 @@
 ### R script to compare several conditions with the SARTools and edgeR packages
 ### Hugo Varet
 ### May 16th, 2018
-### designed to be executed with SARTools 1.6.2
+### designed to be executed with SARTools 1.6.3
 ### run "Rscript template_script_edgeR_CL.r --help" to get some help
 ################################################################################
 

diff --git a/vignettes/SARTools.rmd b/vignettes/SARTools.rmd
@@ -72,7 +72,7 @@ All the parameters that can be modified by the user are at the beginning of the
  - `varInt`: variable of interest, i.e. biological condition, in the target file (`"group"` by default);
  - `condRef`: reference biological condition used to compute fold-changes (no default, must be one of the levels of `varInt`);
  - `batch`: adjustment variable to use as a batch effect, must be a column of the target file (`"day"` for example, or `NULL` if no batch effect needs to be taken into account);
- - `fitType`: (if use of DESeq2) type of model for the mean-dispersion relationship (`"parametric"` by default, or `"local"`);
+ - `fitType`: (if use of DESeq2) type of model for the mean-dispersion relationship (`"parametric"` by default, or `"local"` or `"mean"`);
  - `cooksCutoff`: (if use of DESeq2) `TRUE` (default) of `FALSE` to execute or not the detection of the outliers [7];
  - `independentFiltering`: (if use of DESeq2) `TRUE` (default) of `FALSE` to execute or not the independent filtering [8];
  - `alpha`: significance threshold applied to the adjusted p-values to select the differentially expressed features (default is `0.05`);